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Dr Charles Foster

Dr Charles Foster

Lecturer
Medicine & Health
School of Biomedical Sciences

Dr Charles Foster is a Bioinformatics Research Associate in the Virology Research Lab at University of New South Wales/Prince of Wales Hospital: http://www.virologyresearch.unsw.edu.au/people/scientists/charles-foster/

Dr Foster completed his Bachelor of Science (Advanced) degree at the University of Sydney, receiving 1st Class Honours and the University Medal for his research into the evolution of the Australian flora. Dr Foster’s PhD research focused heavily on developing bioinformatics skills for research into the evolution of different biological groups, with a specific focus on using phylogenomics to understand the evolution of flowering plants. Dr Foster received an award for the best PhD thesis in his year of completion.

Dr Foster’s previous postdoctoral research focused on using transcriptomics to understand the changes in gene expression that underpin pregnancy in different vertebrate groups (mammals, lizards, sharks). Currently, Dr Foster is responsible for developing pipelines for genomic analysis of viruses, especially SARS-CoV-2, within the Virology Research Laboratory. These duties include routine genomic sequencing of viral samples from positive COVID-19 cases, as well as urgent cases flagged by NSW Health.
Phone
+61-2-9382 9096
E-mail
charles.foster@unsw.edu.au
Location
POW & UNSW Virology Research Laboratory Prince of Wales Hospital Level 3, Clinical Sciences Building High Street, Randwick NSW 2031, Australia
  • Journal articles | 2024
    Beasley-Hall PG; Kinjo Y; Rose HA; Walker J; Foster CSP; Kovacs TGL; Bourguignon T; Ho SYW; Lo N, 2024, 'Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life', Insect Science, http://dx.doi.org/10.1111/1744-7917.13339
    Journal articles | 2024
    Egilmezer E; Hamilton ST; Foster CSP; Marschall M; Rawlinson WD, 2024, 'Human cytomegalovirus (CMV) dysregulates neurodevelopmental pathways in cerebral organoids', Communications Biology, 7, http://dx.doi.org/10.1038/s42003-024-05923-1
    Journal articles | 2024
    Harvey E; Foster CSP, 2024, 'Emerging viral threats in Australia', Microbiology Australia, 45, pp. 32 - 37, http://dx.doi.org/10.1071/MA24010
    Journal articles | 2024
    Lau KA; Foster CSP; Theis T; Draper J; Sullivan MJ; Ballard S; Rawlinson WD, 2024, 'Continued improvement in the development of the SARS-CoV-2 whole genome sequencing proficiency testing program', Pathology, 56, pp. 717 - 725, http://dx.doi.org/10.1016/j.pathol.2024.02.010
    Journal articles | 2024
    Walker GJ; Foster CSP; Sevendal A; Domazetovska A; Kamalakkannan A; Williams PCM; Kim KW; Condylios A; Stelzer-Braid S; Bartlett AW; Rawlinson W, 2024, 'Clinical, Genomic, and Immunological Characterization of RSV Surge in Sydney, Australia, 2022', Pediatrics, 153, http://dx.doi.org/10.1542/peds.2023-063667
    Journal articles | 2023
    Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fichter C; Lopez JA; Chandra D; Naing Z; Caguicla J; Li D; Walker G; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Foster CSP; Sato K; Lee S; Song Y; Mao L; Sigmund A; Phu A; Vande More AM; Hunt S; Douglas M; Caterson I; Britton W; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett NW; Darley D; Matthews G; Stark DJ; Petoumenos K; Rawlinson WD; Murrell B; Brilot F; Cunningham AL; Kelleher AD; Aggarwal A; Turville SG, 2023, 'Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level', eBioMedicine, 90, http://dx.doi.org/10.1016/j.ebiom.2023.104545
    Journal articles | 2023
    Foster CSP; Bull RA; Tedla N; Santiago F; Agapiou D; Adhikari A; Walker GJ; Shrestha LB; Van Hal SJ; Kim KW; Rawlinson WD, 2023, 'Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak', Viruses, 15, http://dx.doi.org/10.3390/v15020522
    Journal articles | 2023
    Zufan SE; Lau KA; Donald A; Hoang T; Foster CSP; Sikazwe C; Theis T; Rawlinson WD; Ballard SA; Stinear TP; Howden BP; Jennison AV; Seemann T, 2023, 'Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance', Microbial Genomics, 9, http://dx.doi.org/10.1099/mgen.0.001146
    Journal articles | 2022
    Aggarwal A; Akerman A; Milogiannakis V; Silva MR; Walker G; Stella AO; Kindinger A; Angelovich T; Waring E; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Jean T; Foster CSP; Christ D; Hoppe AC; Munier ML; Darley D; Churchill M; Stark DJ; Matthews G; Rawlinson WD; Kelleher AD; Turville SG, 2022, 'SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern', eBioMedicine, 84, http://dx.doi.org/10.1016/j.ebiom.2022.104270
    Journal articles | 2022
    Aggarwal A; Stella AO; Walker G; Akerman A; Esneau C; Milogiannakis V; Burnett DL; McAllery S; Silva MR; Lu Y; Foster CSP; Brilot F; Pillay A; Van Hal S; Mathivanan V; Fichter C; Kindinger A; Hoppe AC; Munier ML; Amatayakul-Chantler S; Roth N; Coppola G; Symonds GP; Schofield P; Jackson J; Lenthall H; Henry JY; Mazigi O; Jäck HM; Davenport MP; Darley DR; Matthews GV; Khoury DS; Cromer D; Goodnow CC; Christ D; Robosa R; Starck DJ; Bartlett NW; Rawlinson WD; Kelleher AD; Turville SG, 2022, 'Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia', Nature Microbiology, 7, pp. 896 - 908, http://dx.doi.org/10.1038/s41564-022-01135-7
    Journal articles | 2022
    Beasley-Hall P; Bertozzi T; Bradford T; Foster C; Jones K; Humphreys W; Austin A; Cooper S, 2022, 'Stressed out underground?: Illuminating the genomic response to heat stress in surface and subterranean predaceous diving beetles', ARPHA Conference Abstracts, 5, http://dx.doi.org/10.3897/aca.5.e90170
    Journal articles | 2022
    Beasley-Hall PG; Bertozzi T; Bradford TM; Foster CSP; Jones K; Tierney SM; Humphreys WF; Austin AD; Cooper SJB, 2022, 'Differential transcriptomic responses to heat stress in surface and subterranean diving beetles', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-20229-0
    Journal articles | 2022
    Foster CSP; Madden M; Chan R; Agapiou D; Bull RA; Rawlinson WD; Van Hal SJ, 2022, 'SARS-CoV-2 N-gene mutation leading to Xpert Xpress SARS-CoV-2 assay instability', Pathology, 54, pp. 499 - 501, http://dx.doi.org/10.1016/j.pathol.2022.02.001
    Journal articles | 2022
    Foster CSP; Stelzer-Braid S; Deveson IW; Bull RA; Yeang M; Au JP; Ruiz Silva M; van Hal SJ; Rockett RJ; Sintchenko V; Kim KW; Rawlinson WD, 2022, 'Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia', Viruses, 14, http://dx.doi.org/10.3390/v14020185
    Journal articles | 2022
    Foster CSP; Van Dyke JU; Thompson MB; Smith NMA; Simpfendorfer CA; Murphy CR; Whittington CM, 2022, 'Different Genes are Recruited during Convergent Evolution of Pregnancy and the Placenta', Molecular Biology and Evolution, 39, http://dx.doi.org/10.1093/molbev/msac077
    Journal articles | 2022
    Kim KW; Wang X; Adhikari A; Yeang M; Jenkins F; Naing Z; Walker GJ; Foster CSP; Stelzer-Braid S; Deveson I; Craig ME; Tedla N; Bull RA; Martinello M; Pinto AN; Chan R; Turville S; Rawlinson WD; van Hal S, 2022, 'Persistent high-level shedding of cultivable SARS-CoV-2 Delta virus 33 days after onset of COVID-19 in a hospitalized patient with pneumonia', Journal of Medical Virology, 94, pp. 4043 - 4046, http://dx.doi.org/10.1002/jmv.27832
    Journal articles | 2022
    Shrestha LB; Foster C; Rawlinson W; Tedla N; Bull RA, 2022, 'Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission', Reviews in Medical Virology, 32, http://dx.doi.org/10.1002/rmv.2381
    Journal articles | 2022
    Wong DD; van Zuylen WJ; Novos T; Stocker S; Reuter SE; Au J; Foster CSP; Day RO; Horvath AR; Endre Z; Rawlinson WD, 2022, 'Detection of Ganciclovir-Resistant Cytomegalovirus in a Prospective Cohort of Kidney Transplant Recipients Receiving Subtherapeutic Valganciclovir Prophylaxis', Microbiology Spectrum, 10, http://dx.doi.org/10.1128/spectrum.02684-21
    Journal articles | 2021
    Foster CSP; Rawlinson W, 2021, 'Rapid spread of a SARS-CoV-2 Delta variant with a frameshift deletion in ORF7a', , http://dx.doi.org/10.1101/2021.08.18.21262089
    Journal articles | 2021
    Foster CSP; Stelzer-Braid S; Deveson I; Bull R; Yeang M; Phan-Au J; Silva MR; van Hal S; Rockett R; Sintchenko V; Kim KW; Rawlinson W, 2021, 'Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia', , http://dx.doi.org/10.1101/2021.08.19.21262296
    Journal articles | 2021
    Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 2021, 'Background, testing methods, and laboratory approaches to SARS coronavirus-2 (SARS-CoV-2) and Covid19', Pathology, 53, pp. S7 - S7, http://dx.doi.org/10.1016/j.pathol.2021.05.025
    Journal articles | 2021
    Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 2021, 'Background, testing methods, and laboratory approaches to SARS coronavirus-2 (SARS-CoV-2) and covid19', Pathology, 53, pp. S17 - S17, http://dx.doi.org/10.1016/j.pathol.2021.05.060
    Journal articles | 2021
    Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 2021, 'Background, testing methods, and laboratory approaches to sars coronavirus-2 (SARS-CoV-2) and covid19', Pathology, 53, pp. S2 - S3, http://dx.doi.org/10.1016/j.pathol.2021.05.006
    Journal articles | 2021
    Renner MAM; Foster CSP; Miller JT; Murphy DJ, 2021, 'Phyllodes and bipinnate leaves of Acacia exhibit contemporary continental-scale environmental correlation and evolutionary transition-rate heterogeneity', Australian Systematic Botany, 34, pp. 595 - 608, http://dx.doi.org/10.1071/SB21009
    Journal articles | 2021
    Wilson RS; Hunter AH; Camata TV; Foster CSP; Sparkes GR; Moura FA; Santiago PRP; Smith NMA, 2021, 'Simple and reliable protocol for identifying talented junior players in team sports using small-sided games', Scandinavian Journal of Medicine and Science in Sports, 31, pp. 1647 - 1656, http://dx.doi.org/10.1111/sms.13969
    Journal articles | 2020
    Duchêne DA; Tong KJ; Foster CSP; Duchêne S; Lanfear R; Ho SYW, 2020, 'Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference', Molecular Biology and Evolution, 37, pp. 1202 - 1210, http://dx.doi.org/10.1093/molbev/msz291
    Journal articles | 2020
    Foster CSP; Thompson MB; Van Dyke JU; Brandley MC; Whittington CM, 2020, 'Emergence of an evolutionary innovation: Gene expression differences associated with the transition between oviparity and viviparity', Molecular Ecology, 29, pp. 1315 - 1327, http://dx.doi.org/10.1111/mec.15409
    Journal articles | 2020
    Nie Y; Foster CSP; Zhu T; Yao R; Duchêne DA; Ho SYW; Zhong B, 2020, 'Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies', Systematic Biology, 69, pp. 1 - 16, http://dx.doi.org/10.1093/sysbio/syz032
    Journal articles | 2020
    Renner MAM; Foster CSP; Miller JT; Murphy DJ, 2020, 'Increased diversification rates are coupled with higher rates of climate space exploration in Australian Acacia (Caesalpinioideae)', New Phytologist, 226, pp. 609 - 622, http://dx.doi.org/10.1111/nph.16349
    Journal articles | 2020
    Smith NMA; Yagound B; Remnant EJ; Foster CSP; Buchmann G; Allsopp MH; Kent CF; Zayed A; Rose SA; Lo K; Ashe A; Harpur BA; Beekman M; Oldroyd BP, 2020, 'Paternally-biased gene expression follows kin-selected predictions in female honey bee embryos', Molecular Ecology, 29, pp. 1523 - 1533, http://dx.doi.org/10.1111/mec.15419
    Journal articles | 2020
    Yang L; Su D; Chang X; Foster CSP; Sun L; Huang CH; Zhou X; Zeng L; Ma H; Zhong B, 2020, 'Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling', Plant Communications, 1, http://dx.doi.org/10.1016/j.xplc.2020.100027
    Journal articles | 2019
    Foster CSP, 2019, 'Digest: The phylogenetic distance effect: Understanding parasite host switching*', Evolution, 73, pp. 1494 - 1495, http://dx.doi.org/10.1111/evo.13765
    Journal articles | 2019
    van der Merwe M; Yap JYS; Bragg JG; Cristofolini C; Foster CSP; Ho SYW; Rossetto M, 2019, 'Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using DNA sequences', Methods in Ecology and Evolution, 10, pp. 971 - 981, http://dx.doi.org/10.1111/2041-210X.13181
    Journal articles | 2018
    Foster CSP; Henwood MJ; Ho SYW, 2018, 'Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)', Molecular Phylogenetics and Evolution, 127, pp. 156 - 167, http://dx.doi.org/10.1016/j.ympev.2018.05.018
    Journal articles | 2017
    Foster C; Ho S, 2017, 'Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale', , http://dx.doi.org/10.1101/144287
    Journal articles | 2017
    Foster CSP; Ho SYW, 2017, 'Strategies for partitioning clockmodels in phylogenomic dating: Application to the angiosperm evolutionary timescale', Genome Biology and Evolution, 9, pp. 2752 - 2763, http://dx.doi.org/10.1093/gbe/evx198
    Journal articles | 2017
    Foster CSP; Sauquet H; Van Der Merwe M; McPherson H; Rossetto M; Ho SYW, 2017, 'Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale', Systematic Biology, 66, pp. 338 - 351, http://dx.doi.org/10.1093/sysbio/syw086
    Journal articles | 2017
    Sauquet H; Von Balthazar M; Magallón S; Doyle JA; Endress PK; Bailes EJ; Barroso De Morais E; Bull-Hereñu K; Carrive L; Chartier M; Chomicki G; Coiro M; Cornette R; El Ottra JHL; Epicoco C; Foster CSP; Jabbour F; Haevermans A; Haevermans T; Hernández R; Little SA; Löfstrand S; Luna JA; Massoni J; Nadot S; Pamperl S; Prieu C; Reyes E; Dos Santos P; Schoonderwoerd KM; Sontag S; Soulebeau A; Staedler Y; Tschan GF; Wing-Sze Leung A; Schönenberger J, 2017, 'The ancestral flower of angiosperms and its early diversification', Nature Communications, 8, http://dx.doi.org/10.1038/ncomms16047
    Journal articles | 2016
    Duchêne S; Foster CSP; Ho SYW, 2016, 'Estimating the number and assignment of clock models in analyses of multigene datasets', Bioinformatics, 32, pp. 1281 - 1285, http://dx.doi.org/10.1093/bioinformatics/btw005
    Journal articles | 2016
    Foster CSP; Cantrill DJ; James EA; Syme AE; Jordan R; Douglas R; Ho SYW; Henwood MJ, 2016, 'Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)', Australian Systematic Botany, 29, pp. 185 - 196, http://dx.doi.org/10.1071/SB16013
    Journal articles | 2016
    Foster CSP, 2016, 'The evolutionary history of flowering plants', Journal and Proceedings of the Royal Society of New South Wales, 149, pp. 65 - 82
    Journal articles | 2015
    Ho SYW; Tong KJ; Foster CSP; Ritchie AM; Lo N; Crisp MD, 2015, 'Biogeographic calibrations for the molecular clock', Biology Letters, 11, http://dx.doi.org/10.1098/rsbl.2015.0194
    Journal articles | 2014
    Foster CSP; Conn BJ; Henwood MJ; Ho SYW, 2014, 'Molecular data support Orianthera: a new genus of Australian Loganiaceae', TELOPEA, 16, pp. 149 - 158, http://dx.doi.org/10.7751/telopea20147853
    Journal articles | 2014
    Foster CSP; Ho SYW; Conn BJ; Henwood MJ, 2014, 'Molecular systematics and biogeography of Logania R.Br. (Loganiaceae)', Molecular Phylogenetics and Evolution, 78, pp. 324 - 333, http://dx.doi.org/10.1016/j.ympev.2014.06.001
    Journal articles | 2013
    Foster CSP; Conn BJ, 2013, 'Status of Logania imbricata (Guillaumin) Steenis & Leenh. (Loganiaceae)', Telopea, 15, pp. 1 - 4, http://dx.doi.org/10.7751/telopea2013001
  • Preprints | 2023
    Zufan S; Lau K; Donald A; Hoang T; Foster CSP; Sikazwe C; Theis T; Rawlinson W; Ballard S; Stinear T; Howden B; Jennison A; Seemann T, 2023, Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance, http://dx.doi.org/10.1101/2023.02.01.526694
    Preprints | 2022
    Aggarwal A; Akerman A; Milogiannakis V; Silva MR; Walker G; Kidinger A; Angelovich T; Waring E; Amatayakul-Chantler S; Roth N; Coppola G; Yeang M; Jean T; Foster C; Hoppe AC; Ling Munier M; Darley D; Churchill M; Starck D; Christ D; Matthews G; Rawlinson W; Kelleher A; Turville S, 2022, SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern, http://dx.doi.org/10.1101/2022.07.07.22277128
    Preprints | 2022
    Aggarwal A; Akerman A; Milogiannakis V; Silva MR; Walker G; Kidinger A; Angelovich T; Waring E; Amatayakul-Chantler S; Roth N; Yeang M; Jean T; Foster C; Hoppe AC; Munier ML; Darley D; Churchill M; Starck D; Christ D; Matthews G; Rawlinson W; Kelleher A; Turville S, 2022, SARS-CoV-2 Omicron BA.5: Evolving Tropism and Evasion of Potent Humoral Responses and Resistance to Clinical Immunotherapeutics Relative to Viral Variants of Concern, http://dx.doi.org/10.2139/ssrn.4157473
    Preprints | 2022
    Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fitcher C; Lopez J; Chandra D; Naing Z; Caguicla J; Li D; Walker G; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Foster CSP; Sato K; Lee S; Song Y; Mao L; Sigmund A; Phu A; Vande More AM; Hunt S; Douglas M; Caterson I; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett N; Darley D; Matthews G; Stark D; Rawlinson W; Murrell B; Brilot F; Cunningham A; Kelleher A; Aggarwal A; Turville S, 2022, Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sublineages in the face of maturing antibody breadth at the population level, http://dx.doi.org/10.1101/2022.12.06.22283000
    Preprints | 2022
    Foster CSP; Bull R; Tedla N; Santiago F; Agapiou D; Adhikari A; Walker G; Shrestha LB; van Hal S; Kim KW; Rawlinson W, 2022, Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak, http://dx.doi.org/10.1101/2022.09.06.22279658
    Preprints | 2022
    Tai J-H; Low YK; Wang SC-L; Lin H-F; Wang T-Y; Wang J-T; Liu Y-S; Lin Y-Y; Foster CSP; van Hal S; Lai Y-Y; Yeh S-H; Chang S-Y; Chen P-J; Chaw S-M, 2022, Spatial and Temporal Origin of The Third SARS-Cov-2 Outbreak in Taiwan, http://dx.doi.org/10.1101/2022.07.04.498645
    Preprints | 2021
    Beasley-Hall P; Bertozzi T; Bradford T; Foster C; Jones K; Tierney S; Humphreys W; Austin A; Cooper S, 2021, Differential transcriptomic responses to heat stress in surface and subterranean diving beetles, http://dx.doi.org/10.1101/2021.12.12.470823
    Preprints | 2018
    Duchêne D; Tong J; Foster C; Duchêne S; Lanfear R; Ho S, 2018, Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference, http://dx.doi.org/10.1101/467449
    Conference Papers | 1996
    Foster CS; Dana MR; MerayoLloves J; Schaumberg DA, 1996, 'Visual outcomes prognosticators in juvenile rheumatoid arthritis-associated uveitis.', in ARTHRITIS AND RHEUMATISM, LIPPINCOTT-RAVEN PUBL, pp. 186 - 186, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1996VH88300186&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Preprints |
    Tai J-H; Low YK; Lin H-F; Wang T-Y; Lin Y-Y; Foster C; van Hal S; Lai Y-Y; Yeh S-H; Chang S-Y; Chen P-J; Chaw S-M; Wang H-Y, Spatial and Temporal Origin of the Third SARS-CoV-2 Outbreak in Taiwan, http://dx.doi.org/10.2139/ssrn.4201397

  • Establishment of analytical pipelines to accurately capture the genomic variation in viral/bacterial samples
  • Development of best practices for ensuring analytical consistency of genomics analyses between different sites/jurisdictions
  • Researching the spread of SARS-CoV-2 in real-time to understand how emerging pathogens evolve